It looks like this might have been originally designed to work like that in Prompt, possibly because it was considered odd to insert text before the current line and potentially scroll forwards or just to make it consistent with the rest of the code that Prompt inserts (they all overwrite the current word and append the extra text)
I can see how this would be annoying if you're relying on the comments before the stored procedure to be preserved. I'll have a look into this today and see if it's a simple change to make. Otherwise, we currently have a feature request on UserVoice here
, so please do add your vote as we use the votes to help prioritise what to work on next.
A possible work around would be to use the Script as Alter feature (F12) which will keep the comments.